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Yorodumi- PDB-1a3l: CATALYSIS OF A DISFAVORED REACTION: AN ANTIBODY EXO DIELS-ALDERAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a3l | ||||||
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Title | CATALYSIS OF A DISFAVORED REACTION: AN ANTIBODY EXO DIELS-ALDERASE-TSA-INHIBITOR COMPLEX AT 1.95 A RESOLUTION | ||||||
Components |
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Keywords | IMMUNOGLOBULIN / DIELS-ALDER / DISFAVORED REACTION / CATALYTIC ANTIBODY | ||||||
Function / homology | Function and homology information Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Heine, A. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 1998 Title: An antibody exo Diels-Alderase inhibitor complex at 1.95 angstrom resolution. Authors: Heine, A. / Stura, E.A. / Yli-Kauhaluoma, J.T. / Gao, C. / Deng, Q. / Beno, B.R. / Houk, K.N. / Janda, K.D. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3l.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3l.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a3l_validation.pdf.gz | 859.1 KB | Display | wwPDB validaton report |
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Full document | 1a3l_full_validation.pdf.gz | 863.8 KB | Display | |
Data in XML | 1a3l_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1a3l_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3l ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3l | HTTPS FTP |
-Related structure data
Related structure data | 1bbjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23806.480 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 13G5 MURINE HYBRIDOMA / References: GenBank: 1911624, UniProt: P01837*PLUS |
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#2: Antibody | Mass: 23200.771 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 13G5 MURINE HYBRIDOMA / References: EMBL: Y08011, UniProt: P01869*PLUS |
#3: Chemical | ChemComp-CFC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 52 % | |||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: PT COATED FUSED SILICA X-RAY MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 32813 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rsym value: 0.039 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 10 / Rsym value: 0.127 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 188444 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.127 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BBJ Resolution: 1.95→10 Å / Num. parameters: 14607 / Num. restraintsaints: 14033 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995) 53-56 THERE WAS NO CLEAR DENSITY FOR AN EXTERNAL LOOP REGION IN THE CONSTANT HEAVY CHAIN (H 129 - H 135).
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Solvent computation | Solvent model: MOEWS&KRETSINGER,J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 3173 / Occupancy sum non hydrogen: 3614 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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